Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

<prev • 6,132 results • page 2 of 614 • next >
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Answer: A: Remove sequences with stop codons from FASTA file
... [linearize][1] and filter with awk awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' input.fa | awk -F '\t' '!($2 ~ /\*/)' | tr "\t" "\n" [1]: https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345 ...
written 11 days ago by Pierre Lindenbaum96k
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Comment: C: How to print two lines of several files to a new file with the speicific order?
... use /bin/bash please ...
written 12 days ago by Pierre Lindenbaum96k
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Comment: C: How to print two lines of several files to a new file with the speicific order?
... what is your shell ? ...
written 12 days ago by Pierre Lindenbaum96k
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Comment: C: How to print two lines of several files to a new file with the speicific order?
... okay here is the gist that worked on my machine: https://gist.github.com/lindenb/b1e95a593fdc8c71357856f8b15869e6 ...
written 12 days ago by Pierre Lindenbaum96k
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Comment: C: How to print two lines of several files to a new file with speicific order?
... Ah yes, I've reformatted it on the fly. I've just removed a semicolon, can you please try again please. ...
written 12 days ago by Pierre Lindenbaum96k
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Answer: A: How to print two lines of several files to a new file with speicific order?
... using sqlite3: just put your sequence in a database and pull them out. v=1 && \ rm -f db.sqlite3 && \ sqlite3 db.sqlite3 'create table S(name,sequence,num,file);' && \ for F in input1.txt input2.txt input3.txt do awk -v fidx=$v '{if(NR%2==1) {prin ...
written 13 days ago by Pierre Lindenbaum96k
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Comment: C: kernel k-means java code source
... https://www.google.fr/search?q=kernel+k-means+filetype%3Ajava ??? ...
written 13 days ago by Pierre Lindenbaum96k
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Answer: A: Is PICARD CollectInsertSizeMetrics use soft-clipping information to compute the
... it uses the information stored in the BAM file (TLEN): so it's not dependent of picard. https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java#L53 final int insertSize = Math.abs(samRecord.getInferredInsertSize()); ...
written 13 days ago by Pierre Lindenbaum96k
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Answer: A: polyploidy found and not supported by vcftools
... > , so I have to search for them using the numbers of chromosomes and positions. convert your table to bed. (chrom / 0-based-start/ 0-based-end) and use https://samtools.github.io/bcftools/bcftools.html bcftools view --targets-file the.bed input.vcf ...
written 13 days ago by Pierre Lindenbaum96k
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Comment: C: polyploidy found and not supported by vcftools
... > Also, yes the filter file is actually in excel format. there is no magic. Most tools won't be able to use this file. and excel is bad. https://twitter.com/search?q=%23dontuseexcel&src=typd and : ![enter image description here][1] [1]: https://pbs.twimg.com/media/BRjnZqeCIAEl84N.png ...
written 13 days ago by Pierre Lindenbaum96k

Latest awards to Pierre Lindenbaum

Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 6 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How To Combine Two Samtools Commands.
Popular Question 8 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 13 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 19 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Scholar 23 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Scholar 26 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 27 days ago, created an answer that has been accepted. For A: Variant callers reporting different read depth on same alignment
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Great Question 27 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Good Answer 28 days ago, created an answer that was upvoted at least 5 times. For A: Exon Coordinates Of Hg19 Genome Download
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Appreciated 4 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 4 weeks ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Scholar 4 weeks ago, created an answer that has been accepted. For A: Variant callers reporting different read depth on same alignment
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 4 weeks ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs

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